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This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

1. To characterize the spatial phylogenetic structure of communities, Hardy AND Senterre (2007) (J. Ecol., 95, 493-506) partition Gini-Simpson diversity and its generalization, Rao's entropy, defining I-ST and P-ST as the proportion of diversity expressed among sites. 2. Interpreting I-ST as a measure of `differentiation' between sites is inadequate because low values are actually compatible with high differentiation (low species sharing) in species rich communities. To avoid an inadequate use of I-ST, for example in conservation biology, we offer a more literal interpretation: I-ST expresses the `local species identity excess'. Similarly, P-ST expresses the `local phylogenetic similarity excess'. 3. Villeger AND Mouillot (2008) (J. Ecol., 96, 845-848, this issue) argue that the equations of Hardy AND Senterre (2007) to compute diversity are inadequate when sites differ in size, and they provide new expressions weighting sites by their sizes. We argue that whether sites must be weighted equally or not depends on the question being asked. Moreover, actual size and sample size must be distinguished, the latter being important for defining estimators. 4. Synthesis. The formulations given by Hardy AND Senterre (2007) and by Villeger AND Mouillot (2008)are both correct in the specific contexts we detail.

1. Analyzing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species. For instance, an association between species co-occurrence in local communities and their phylogenetic proximity may reveal the action of habitat filtering, niche conservatism and/or competitive exclusion. 2. Different methods were recently proposed to test such community-wide phylogenetic patterns, based on the phylogenetic clustering or overdispersion of the species in a local community. This provides a much needed framework for addressing long standing questions in community ecology as well as the recent debate on community neutrality. The testing procedures are based on (i) a metric measuring the association between phylogenetic distance and species co-occurrence, and (ii) a data set randomization algorithm providing the distribution of the metric under a given `null model'. However, the statistical properties of these approaches are not well-established and their reliability must be tested against simulated data sets. 3. This paper reviews metrics and null models used in previous studies. A `locally neutral' subdivided community model is simulated to produce data sets devoid of phylogenetic structure in the spatial distribution of species. Using these data sets, the consistency of Type I error rates of tests based on 10 metrics combined with nine null models is examined. 4. This study shows that most tests can become liberal (i.e. tests rejecting too often the null hypothesis that only neutral processes structured spatially the local community) when the randomization algorithm breaks down a structure in the original data set unrelated to the null hypothesis to test. Hence, when overall species abundances are distributed non-randomly across the phylogeny or when local abundances are spatially autocorrelated, better statistical performances were achieved by randomization algorithms preserving these structural features. The most reliable randomization algorithm consists of permuting species with similar abundances among the tips of the phylogenetic tree. One metric, RPD-DO, also proved to be robust under most simulated conditions using a variety of null models. 5. Synthesis. Given the suboptimal performances of several tests, attention must be paid to the testing procedures used in future studies. Guidelines are provided to help choosing an adequate test.

Aim In contrast to angiosperms, bryophytes do not appear to have radiated in Macaronesia and the western Mediterranean. We evaluate if: (1) the apparent lack of radiation in bryophytes reflects our failure to recognize cryptic endemic species; (2) bryophytes are characterized by extremely low evolutionary rates; or (3) bryophytes have a high dispersal ability, which prevents genetic isolation. Location Worldwide, with a special emphasis on Macaronesia and the western Mediterranean. Methods Three chloroplast regions were sequenced from samples of the moss Grimmia montana from its entire distribution range. Network analyses, Fst and Nst statistics were used to describe and interpret the phylogeographical signal in the data. Results Despite significant phylogeographical signal in the chloroplast genome, which demonstrates limits to gene flow at the continental scale, repeated sister group relationships observed among accessions from different geographical areas suggest recurrent colonization patterns. These observations are consistent with mounting evidence that intercontinental distributions exhibited by many bryophyte species result from long-distance dispersal rather than continental drift. Madeiran and western Mediterranean island haplotypes are either shared by, or closely related to, European and North American ones. Fst values between Madeira, western Mediterranean islands, North America and Europe are not significantly different from zero, and suggest that Madeira and the south-western Mediterranean are subject to strong transatlantic gene flow. By contrast, haplotypes found in the Canary Islands are shared or closely related to those of populations from south-western Europe or southern Africa. Main conclusions Multiple origins and colonization events are not consistent with the hypothesis of a relictual origin of the Macaronesian moss flora. One possible reason for the failure of taxa that experienced multiple colonization events to radiate is niche pre-emption. We suggest that strong gene flow, coupled with the occupancy of all suitable niches, either by earlier conspecific colonizers or by other species, could be the mechanism preventing island radiation in G. montana and other cryptogams with high long-distance dispersal abilities.

Under the isolation-by-distance model, the strength of spatial genetic structure (SGS) depends on seed and pollen dispersal and genetic drift, which in turn depends on local demographic structure. SGS can also be influenced by historical events such as admixture of differentiated gene pools. We analysed the fine-scale SGS in six populations of a pioneer tree species endemic to Central Africa, Aucoumea klaineana. To infer the impacts of limited gene dispersal, population history and habitat fragmentation on isolation by distance, we followed a stepwise approach consisting of a Bayesian clustering method to detect differentiated gene pools followed by the analysis of kinship-distance curves. Interestingly, despite considerable variation in density, the five populations situated under continuous forest cover displayed very similar extent of SGS. This is likely due to an increase in dispersal distance with decreased tree density. Admixture between two gene pools was detected in one of these five populations creating a distinctive pattern of SGS. In the last population sampled in open habitat, the genetic diversity was in the same range as in the other populations despite a recent habitat fragmentation. This result may due to the increase of gene dispersal compensating the effect of the disturbance as suggested by the reduced extent of SGS estimated in this population. Thus, in A. klaineana, the balance between drift and dispersal may facilitate the maintenance of genetic diversity. Finally, from the strength of the SGS and population density, an indirect estimate of gene dispersal distances was obtained for one site: the quadratic mean parent-offspring distance, sigma(g), ranged between 210 m and 570 m.

In a population of the monogynous, polyandrous ant Cataglyphis cursor, we analysed the spatial genetic structure of queens, colony fathers and workers at a microgeographical scale to infer the extent of sex-biased dispersal and to assess the impact of limited dispersal on the patterns of relatedness within the colony. To this end, four microsatellite markers were scored for the queen and an average of 26 workers from each of 35 mapped colonies. We used pair-wise kinship coefficients between all pairs of genotypes, including the reconstructed colony father genotypes (1) to test and quantify isolation by distance patterns within each sex or caste through the analysis of kinship–distance curves, and (2) to compute the average relatedness between categories of colony members. The kinship–distance curve was much steeper for colony queens than colony fathers, indicating male-biased dispersal. However, colony fathers also displayed a non-random spatial genetic structure, so that even males show some dispersal limitation at the scale of the population, which extends over less than 250 m. The degree of relatedness between the different sexes and castes of colonies was well predicted from the number of mates per queen and the inbreeding of queens, and the impact of limited dispersal was very weak at this scale of observation. We discuss the interest of kinship–distance curves to assess sex-biased dispersal on a local scale and we compare our results with large-scale analyses of genetic structure in Cataglyphis cursor and other monogynous ant species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 465–473.

1 Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2 Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. I-ST, P-ST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. F-ST, N-ST). 3 Two coefficients which express community differentiation among sites from species identity (I-ST) or species phylogeny (P-ST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (Pi(ST)) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4 We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (P-ST > I-ST or Pi(ST) > 0) or phylogenetic overdispersion (P-ST

Oaks are model species for the study of natural introgressive hybridization. High interfertility among oak taxa might result in collective evolution, through transpecific spread of advantageous alleles, challenging the standard concept of species. Nine highly polymorphic microsatellite (nuSSR) loci were analysed in three mixed oak populations of Quercus pyrenaica and Quercus petraea (Montejo, Somosierra and Robregordo) with different density and hybridization rates. Both leaf morphology and molecular markers were used to assess individual admixture rates. Insights about the relative effect of density and hybridization rates on fine-scale spatial genetic structure (SGS) were obtained from autocorrelograms and Sp statistics. Differences in SGS among populations were higher than between species. These differences cannot be attributed solely to census densities but also relate to other factors, such as the spatial configuration of the population. Hybridization was an important factor shaping within-population spatial genetic structure, and an interspecific component of SGS was found in Somosierra. Indirect estimates of historical gene flow in Montejo were compared with actual values of gene dispersal assessed by parentage analysis in a former study. Similar values were found for current and historical gene flow in both species, which might reflect demographical stability.

• 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 fl ow patterns and the structure ofgenetic diversity.• Methods and Results: From a genomic library obtained by next-generation sequencing, seven monomorphic and 14 polymorphicmicrosatellite loci were developed. The polymorphic microsatellites displayed two to 27 alleles (mean 11.4; expectedheterozygosity range 0.283–0.940, mean 0.736) in one population from southeastern Cameroon. Genotypes were typical ofan outbreeding diploid species, although null alleles explain a signifi cant heterozygote defi cit in three loci. Cross-amplifi cationin 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, populationstructure, and demographic history of T. superba in tropical African forests., SCOPUS: ar.j, info:eu-repo/semantics/published

Background and aims – Prior to European colonisation of Central Africa, human populations were dispersed through the forests, where they practiced slash-and-burn cultivation. From the 19 th century they were progressively concentrated in villages along roads, leaving large areas of forest derelict. In south-western Cameroon, and elsewhere in Central Africa, forest canopy is dominated by long-lived light-demanding tree species, suggesting a possible role of human disturbance. The aim of this study was to bring new insights into the possible effect of historical human disturbances in terms of timing and spatial extent on the current forest composition. Location – Wet evergreen littoral forest in south-western Cameroon. Methods and key results – A combined vegetation sampling and archaeobotanical survey were conducted. Potsherds, oil-palm endocarps, and charcoal were found throughout the study area, suggesting generalised human occupation and anthropogenic fire. Human occupancy occurred in two periods: between 2200 and 1500 BP, and, more recently, beginning three centuries ago. High frequency of fire and the presence of Elaeis guineensis both dated recently (between 260 and 145 BP) suggest slash-and-burn shifting cultivation practices. These human-induced disturbances may coincide with the age of the current emergent light-demanding species, the age of which can be estimated around 200 years, or with the phases of drying climate recorded in the Central African forest in the early 18 th century. Conclusions – These results support the idea that historical human disturbances are one of the major factors that shaped the current forest composition in Central Africa.

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., SCOPUS: ar.j, info:eu-repo/semantics/published

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.

Aims To identify the relative contributions of environmental determinism, dispersal limitation and historical factors in the spatial structure of the floristic data of inselbergs at the local and regional scales, and to test if the extent of species spatial aggregation is related to dispersal abilities. Location Rain forest inselbergs of Equatorial Guinea, northern Gabon and southern Cameroon (western central Africa). Methods We use phytosociological releves and herbarium collections obtained from 27 inselbergs using a stratified sampling scheme considering six plant formations. Data analysis focused on Rubiaceae, Orchidaceae, Melastomataceae, Poaceae, Commelinaceae, Acanthaceae, Begoniaceae and Pteridophytes. Data were investigated using ordination methods (detrended correspondence analysis, DCA; canonical correspondence analysis, CCA), Sorensen's coefficient of similarity and spatial autocorrelation statistics. Comparisons were made at the local and regional scales using ordinations of life-form spectra and ordinations of species data. Results At the local scale, the forest-inselberg ecotone is the main gradient structuring the floristic data. At the regional scale, this is still the main gradient in the ordination of life-form spectra, but other factors become predominant in analyses of species assemblages. CCA identified three environmental variables explaining a significant part of the variation in floristic data. Spatial autocorrelation analyses showed that both the flora and the environmental factors are spatially autocorrelated: the similarity of species compositions within plant formations decreasing approximately linearly with the logarithm of the spatial distance. The extent of species distribution was correlated with their a priori dispersal abilities as assessed by their diaspore types. Main conclusions At a local scale, species composition is best explained by a continuous cline of edaphic conditions along the forest-inselberg ecotone, generating a wide array of ecological niches. At a regional scale, these ecological niches are occupied by different species depending on the available local species pool. These subregional species pools probably result from varying environmental conditions, dispersal limitation and the history of past vegetation changes due to climatic fluctuations.

We used chloroplast polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad-leaved wind-pollinated and wind-dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR-RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash’s life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (G ST = 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south-eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.

Tree species distribution has been investigated along 45 km of line transects in the tropical rain forest of the Dja Fauna Reserve in Cameroon. The spatial patterns were expressed by the probabilities that two trees are conspecific according to the distance separating them, providing information on the degree of species clumping as well as on alpha- and beta-diversity. Our objective was to assess the relative importance of habitat heterogeneity and limited dispersal in determining these patterns by: (1) comparing the patterns observed within and across major habitats; (2) comparing the patterns with the ones expected under a neutral hypothesis where limited dispersal is the sole factor. Although, habitat heterogeneity affected the distribution of many species, our results suggest that limited dispersal was the major factor affecting the degree of species clumping. The pattern observed was similar to the one found in Amazonia by Condit et al. [Science 295 (2002) 666]. We discuss the relevance of neutral models of tree communities to study the dispersal abilities of tree species. # 2004 Elsevier B.V. All rights reserved.

Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an ‘ Sp ’ statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.

Ten microsatellite loci were used to investigate the impact of human activity on the spatial and temporal genetic structure of Vitellaria paradoxa (Sapotaceae), a parkland tree species in agroforestry systems in southern Mali. Two stands (forest and fallow) and three cohorts (adults, juveniles and natural regeneration) in each stand were studied to: (i) compare their levels of genetic diversity (gene diversity, HE; allelic richness, Rs; and inbreeding, FIs); (ii) assess their genetic differentiation (FsT); and (iii) compare their levels of spatial genetic structuring. Gene diversity parameters did not vary substantially among stands or cohorts, and tests for bottleneck events were nonsignificant. The inbreeding coefficients were not significantly different from zero in most cases (FIS = -0.025 in forest and 0.045 in fallow), suggesting that the species is probably outbreeding. There was a weak decrease in FIS with age, suggesting inbreeding depression. Differentiation of stands within each cohort was weak (FST = 0.026, 0.0005, 0.010 for adults, juveniles and regeneration, respectively), suggesting extensive gene flow. Cohorts within each stand were little differentiated (FST = -0.001 and 0.001 in forest and fallow, respectively). The spatial genetic structure was more pronounced in fallow than in forest where adults showed no spatial structuring. In conclusion, despite the huge influence of human activity on the life cycle of Vitellaria paradoxa growing in parkland systems, the impact on the pattern of genetic variation at microsatellite loci appears rather limited, possibly due to the buffering effect of extensive gene flow between unmanaged and managed populations. (Resume d'auteur)

An extensive allozyme survey was conducted within a natural ''meta'' population of the native North American annual legume, Chamaecrista fasciculata (Leguminosae) to quantify genetic structure at different spatial scales. Gene flow was then estimated by a recently developed indirect method based on a continuous population model, using pairwise kinship coefficients between individuals. The indirect estimates of gene flow, quantified in terms of neighborhood size, with an average value on the order of 150 individuals, were concordant among different spatial scales (subpopulation, population, metapopulation). This gene-flow value lies within the range of direct estimates previously documented from observations of pollen and seed dispersal for the same metapopulation. Monte Carlo simulations using the direct measures of gene flow as parameters further demonstrated that the observed spatial pattern of allozyme variation was congruent with a model of isolation by distance. Combining previously published estimates of pollen dispersal distances with kinship coefficients from this study, we quantified biparental inbreeding relative to either a single subpopulation or the whole metapopulation. At the level of a neighborhood, little biparental inbreeding was observed and most departure from Hardy-Weinberg genotypic proportions was explained by self-fertilization, whereas both selfing and biparental inbreeding contributed to nonrandom mating at the metapopulation level. Gene flow was also estimated from indirect methods based on a discontinuous population structure model. We discuss these results with respect to the effect of a patchy population structure on estimation of gene flow.

Scorodophloeus zenkeri is a tropical tree from mature rainforests of Central Africa, locally threatened by overexploitation. Ten nuclear microsatellite markers, amplifiable in two multiplexed reactions, were developed and characterized in one population. The levels of polymorphism observed (3–15 alleles per locus, expected heterozygosity ranging from 0.198 to 0.905) point at the promising application of the markers for conservation purposes regarding the location of past forest refugia, assessment of mating system and evaluation of genetic diversity in isolated and threatened populations.

The Centaurea jacea aggregate is a polymorphic polyploid complex whose taxonomic treatment is still controversial. A numerical taxonomic approach was applied to 394 individuals of known ploidy level, from 19 populations, based on the main diagnostic characters proposed in earlier revisions. Populations from xeric grasslands were not considered. Principal Component Analysis shows that variation within the complex is continuous. UPGMA Cluster Analysis based on population means supports the recognition of three groups of populations. However, the limits between these groups are blurred to a considerable extent due to extensive within-population polymorphism. It is argued that the Belgian populations of Centaurea jacea occurring in mesic grasslands should be treated as a single species, with three subspecies. The two extremes of the morphological gradient can be referred to as C. jacea subsp. jacea and C. jacea subsp. nigra, with C. jacea subsp. pratensis occupying an intermediate position. Most populations from Belgium are tetraploid, a diploid chromosome number being found only in populations of C. jacea subsp. nigra from the Ardennes massif. On average, diploids grow at higher altitude and on more acidic soils than tetraploids. Finally, a key to the three subspecies is provided., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

Taxonomic classification based on morphology alone can prove difficult. This is the case of the polymorphic forest tree species Santiria trimera in Africa, whose classification has remained controversial for over a century. Studies combining chloroplast and nuclear DNA sequences show the existence of several phylogenetic clades in this taxon, with some occurring in sympatry in western Central Africa suggesting the existence of at least two species. By combining genetic and morphological markers, we aim to assess the species delimitation in the Santiria species complex. Morphological trait (trunk, leaflet, flower and fruit characteristics) analysis using 223 standing individuals and 103 herbarium samples were combined with genetic analyses using 479 individuals genotyped at eight microsatellite markers. Genetic clusters were identified using Bayesian assignment in order to delimit species following the Biological Species Concept and to identify distinctive characters from morphometric analyses in retrospect. Three genetic clusters were identified and found to occur in sympatry. The type of inflorescence and the colour of unripe fruit were the most discriminant morphological traits among those genetic clusters, while many quantitative traits showed overlapping distributions between genetic clusters and explain the difficulty encountered by previous botanists to resolve the taxonomy of Santiria. The combination of genetic and morphological data suggests the presence of three species within the taxon Santiria trimera from western Central Africa. This work should guide a taxonomic revision within the genus Santiria in Africa., SCOPUS: ar.j, info:eu-repo/semantics/published

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 nextgeneration 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., SCOPUS: ar.j, info:eu-repo/semantics/published

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., SCOPUS: ar.j, info:eu-repo/semantics/published

Computer simulations of genetic data are increasingly used to investigate the impact of complex historical scenarios on patterns of genetic variation. Yet, in most empirical studies, relatively large portions of species ranges are often treated as panmictic populations, ignoring the underlying spatial context. In some cases, however, a more accurate spatial model is required. We use a spatially explicit model of coalescence (easily constructed by overlaying a two-dimensional grid on maps displaying an estimate of past and current species ranges) to evaluate the potential of several summary statistics to differentiate three typical phylogeographic scenarios. We first explore the variation of each summary statistic within the boundaries of each phylogeographic scenario, and identify those that appear most promising for a comparison of historical scenarios and/or to infer historical parameters. We then combine a selected set of summary statistics in a single chi-square statistic and evaluate whether it can be used to differentiate past geographic fragmentation or range expansion from a simple scenario of isolation by distance. We also investigate the benefits of using a spatially explicit model by comparing its performance to alternative models that are less spatially explicit (lower geographic resolution). The results identify conditions in which each summary statistic is useful to infer the evolution of a species range, and allow us to validate our spatially explicit model of coalescence and our procedure to compare simulated and observed sequence data. We also provide a detailed description of the spatially explicit model of coalescence used, which is currently lacking.

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-bydistance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world. © 2014 Manel et al., SCOPUS: ar.j, info:eu-repo/semantics/published

Comparative phylogeography is an effective approach to assess the evolutionary history of biological communities. We used comparative phylogeography in fourteen tree taxa from Lower Guinea (Atlantic Equatorial Africa) to test for congruence with two simple evolutionary scenarios based on physio-climatic features 1) the W-E environmental gradient and 2) the N-S seasonal inversion, which determine climatic and seasonality differences in the region. We sequenced the trnC-ycf6 plastid DNA region using a dual sampling strategy: fourteen taxa with small sample sizes (dataset 1, mean n = 16/taxon), to assess whether a strong general pattern of allele endemism and genetic differentiation emerged; and four taxonomically well-studied species with larger sample sizes (dataset 2, mean n = 109/species) to detect the presence of particular shared phylogeographic patterns. When grouping the samples into two alternative sets of two populations, W and E, vs. N and S, neither dataset exhibited a strong pattern of allelic endemism, suggesting that none of the considered regions consistently harboured older populations. Differentiation in dataset 1 was similarly strong between W and E as between N and S, with 3-5 significant F ST tests out of 14 tests in each scenario. Coalescent simulations indicated that, given the power of the data, this result probably reflects idiosyncratic histories of the taxa, or a weak common differentiation pattern (possibly with population substructure) undetectable across taxa in dataset 1. Dataset 2 identified a common genetic break separating the northern and southern populations of Greenwayodendron suaveolens subsp. suaveolens var. suaveolens, Milicia excelsa, Symphonia globulifera and Trichoscypha acuminata in Lower Guinea, in agreement with differentiation across the N-S seasonal inversion. Our work suggests that currently recognized tree taxa or suspected species complexes can contain strongly differentiated genetic lineages, which could lead to misinterpretation of phylogeographic patterns. Therefore the evolutionary processes of such taxa require further study in African tropical rainforests., Journal Article, SCOPUS: ar.j, info:eu-repo/semantics/published

Coexistence of species in tropical forests remains an open debate in community ecology. Two main substrates, sandy and clay soils, exist in sites harboring semi-deciduous forests in the central Congo Basin. The way this edaphic heterogeneity affects species occurrences and abundances was investigated. Sampling plots were established on each of the soils in Yoko, a natural forest reserve located in the surrounding of Kisangani (eastern D.R. Congo). Results showed that species react in different ways according to the considered soil. Some species appear to be “edaphic specialists” by their exclusive occurrence or preference towards a given soil. This is the case for species like Scorodophloeus zenkeri, Cynometra hankei, Prioria balsamiferum on sandy soils whereas Alstonia boonei, Antiaris toxicaria, etc. prefer clay substrates. Many others expressed no preference at all. We computed species accumulation curves and tested for the local diversity (Fisher alpha index) among soils. Communities on clay soils appear to be rich and more diversified.&nbsp

Analysis of the spatial genetic structure within continuous populations in their natural habitat can reveal acting evolutionary processes. Spatial autocorrelation statistics are often used for this purpose, but their relationships with population genetics models have not been thoroughly established. Moreover, it has been argued that the dependency of these statistics on variation in mutation rates among loci strongly limits their interest for inferential purposes. In the context of an isolation by distance process, we describe relationships between a descriptor of the spatial genetic structure used in empirical studies, Moran's I statistic and population genetics parameters. In particular, we point out that, when Moran's I statistic is used to describe correlation in allele frequencies at the individual level, it provides an estimator of Wright's coefficient of relationship. We also show that the latter parameter, as a descriptor of genetic structure, is not influenced by selfing rate or ploidy level. Under specific finite population models, numerical simulations show that values of Moran's I statistic can be predicted from analytical theory. These simulations are also used to estimate the time taken to approach a structure at equilibrium. Finally, we discuss the conditions under which spatial autocorrelation statistics are little influenced by variation in mutation rates, so that they could be used to estimate gene dispersal parameters.

Rapid geographic range expansions can have dramatic effects on the distribution of genetic diversity, both within and among populations. Based on field records collected over the past two decades in Western Europe, we report on the rapid geographic range expansion in Colletes hederae, a solitary bee species. To characterize how this expansion shaped the distribution of genetic diversity within and among populations, we performed a genetic analysis based on the sequencing of three nuclear loci (RNAp, CAD and WgL). We then simulated the evolution of DNA sequences under a spatially explicit model of coalescence to compare different hypotheses regarding the mode of colonization associated with this rapid expansion and to identify those that are most consistent with the observed molecular data. Our genetic analyses indicate that the range expansion was not associated with an important reduction in genetic diversity, even in the most recently colonized area in the United Kingdom. Moreover, little genetic differentiation was observed among populations. Our comparative analysis of simulated data sets indicates that the observed genetic data are more consistent with a demographic scenario involving relatively high migration rates than with a scenario based on a high reproduction rate associated with few migrants. In the light of these results, we discuss the factors that might have contributed to the rapid geographic range expansion of this pollen-specialist solitary bee species across Western Europe., JOURNAL ARTICLE, SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

Background and aims – Recent molecular studies suggest the polyphyly of Angraecum and the unnaturalness of some of its sections, as exemplified by sect. Pectinaria, which has species in two well-separated clades, one in Madagascar and the other in continental Africa. However, species delimitation among the five continental African members remained problematic due to morphological variability. In preparation for the taxonomic revision of this group, we used morphological and molecular data to re-assess the circumscription of each species, and to evaluate their monophyly and relationships to one another. Methods – A total of 59 alcohol-preserved specimens were used to perform multivariate analyses on 37 morphological characters. DNA sequences from one nuclear (ITS-1) and five plastid regions ( matK, rps16, trnL – F, trnC – petN and ycf1 ) were analyzed using Parsimony and Bayesian methods. Key results – The morphometric study revealed five distinct morphospecies that correspond to the concepts of the currently recognized species. Angraecum doratophyllum and A. subulatum are the most distinct morphologically, whereas A. atlanticum, A. gabonense and A. pungens are most similar to one another. Phylogenetic analyses using a combined data set of the six markers yielded highly resolved, congruent trees with strong branch support. The polyphyly of A . sect. Pectinaria is confirmed, with continental African members appearing to be most closely related to sect. Dolabrifolia, found exclusively in Africa. The multiple accessions of A. doratophyllum, A. gabonense, A. pungens and A. subulatum each formed a well-supported clade. Parsimony and Bayesian analyses placed A. atlanticum and A. pungens in a subclade within which samples of A. pungens were nested but those of A. atlanticum formed a grade. These two species can be easily distinguished morphologically by leaf dimensions and flower length, but broader sampling in continental Africa is needed to test whether individuals recognized as A. atlanticum might represent two distinct taxa.

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation - coastal or swamp vs terra firme - in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees. © 2013 Macmillan Publishers Limited All rights reserved.

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., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science. © 2012 CNRS. Biological Reviews © 2012 Cambridge Philosophical Society.

International audience; A five-day international workshop was recently convened at the Universite' des Sciences et Techniques de Masuku in Gabon to enhance international collaboration among Central African, US and European scientists, conservation professionals and policy makers. The overall aims of the workshop were to: (1) discuss emerging priorities in biodiversity and conservation genetics research across Central Africa, and (2) create new networking opportunities among workshop participants. Here we provide a brief overview of the meeting, outline the major recommendations that emerged from it, and provide informatio n on new networking opportunities through themeeting web site.

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

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.

The invasive alien knotweeds, Fallopia spp. (Polygonaceae), are some of the most troublesome invasive species in Europe and North America. Invasive success in Fallopia may be enhanced by multiple hybridization events. We examined the pattern of hybridization and its evolutionary consequences in Belgium with a concerted analysis of ploidy levels (chromosome counts and flow cytometry), morphological variation, and genetic variation (RAPDs). At least four taxa with different ploidy levels were part of the pattern of invasion in Belgium. Hybrid F. 3bohemica with various chromosome numbers restored the genotypic diversity that was lacking in the parental species. Hybrid genotypes were mainly assigned to a specific genetic pool and not to a mixture between the genetic pools of the putative parental species as would be expected for hybrids. Parental species and hexaploid hybrids differed significantly for a set of well-defined morphological characters, enabling future researchers to distinguish these taxa. On the basis of our results, the importance of hybridization has probably been underestimated in large parts of the adventive range of alien Fallopia species, pointing to the need for concerted molecular and morphological analyses in the study of the evolutionary consequences of hybridization.

Invasive species are a threat for ecosystems worldwide, especially oceanic islands. Predicting the invasive potential of introduced species remains difficult, and only a few studies have found traits correlated to invasiveness. We produced a molecular phylogenetic dataset and an ecological trait database for the entire Azorean flora and find that the phylogenetic nearest neighbour distance (PNND), a measure of evolutionary relatedness, is significantly correlated with invasiveness. We show that introduced plant species are more likely to become invasive in the absence of closely related species in the native flora of the Azores, verifying Darwin's 'naturalization hypothesis'. In addition, we find that some ecological traits (especially life form and seed size) also have predictive power on invasive success in the Azores. Therefore, we suggest a combination of PNND with ecological trait values as a universal predictor of invasiveness that takes into account characteristics of both introduced species and receiving ecosystem.

International audience; The effect of selection on patterns of genetic structure within and between populations may be studied by contrasting observed patterns at the genes targeted by selection with those of unlinked neutral marker loci. Local directional selection on target genes will produce stronger population genetic structure than at neutral loci, whereas the reverse is expected for balancing selection. However, theoretical predictions on the intensity of this signal under precise models of balancing selection are still lacking. Using negative frequency-dependent selection acting on self-incompatibility systems in plants as a model of balancing selection, we investigated the effect of such selection on patterns of spatial genetic structure within a continuous population. Using numerical simulations, we tested the effect of the type of self-incompatibility system, the number of alleles at the selfincompatibility locus and the dominance interactions among them, the extent of gene dispersal, and the immigration rate on spatial genetic structure at the selected locus and at unlinked neutral loci. We confirm that frequency-dependent selection is expected to reduce the extent of spatial genetic structure as compared to neutral loci, particularly in situations with low number of alleles at the self-incompatibility locus, high frequency of codominant interactions among alleles, restricted gene dispersal and restricted immigration from outside populations. Hence the signature of selection on spatial genetic structure is expected to vary across species and populations, and we show that empirical data from the literature as well as data reported here on three natural populations of the herb Arabidopsis halleri confirm these theoretical results.

The production of diploid daughters from unfertilized eggs can be achieved through various cytological mechanisms. Under apomictic parthenogenesis, meiosis is suppressed, and the absence of recombination or re-assortment of alleles leads to the production of a ‘true clone' of the mother. By contrast, under automictic parthenogenesis, the first stages of meiosis are conserved and diploidy is restored by fusion of two nuclei originating from the same primary oocyte (terminal, central or random fusion) or by gamete duplication (Suomalainen et al., 1987). Automictic parthenogenesis increases homozygosity at each generation, but the rate of increase depends on the cytological mechanism restoring diploidy. In a previous paper in Heredity, we determined the mode of thelytokous parthenogenesis in the ant Cataglyphis cursor, by comparing the observed generational increase in homozygosity at several informative loci with theoretical expectations (Table 1 in Pearcy et al., 2006). We argued that the expected rate of transition from heterozygosity to homozygosity at each generation was 0.33 (rather than 0.50) for loci with high recombination under terminal and central fusion. Here we clarify the reasoning behind the calculations. During gametogenesis, the duplicated homologous chromosomes of the 4n primary oocyte pair at the prophase of meiosis I and crossovers can occur between chromatids (Figure 1a). The probability of crossover in the region between the centromere and a given locus increases with the distance between the two. However, when multiple crossovers occur, the original location of the alleles can, by chance, be restored (locus 2 in Figure 1b). Also, if alleles are swapped for both chromatid pairs, the effects of the two recombination events cancel out each other (locus 2 in Figure 1c). In short, the probability that the alleles are effectively swapped between homologous chromosomes is not equal to the probability of observing at least one crossover. Figure 1 Effects of recombination during oogenesis. Chromosomal crossovers (black triangles) result in alleles being swapped between homologous chromatids (a), leading to alternate allele segregation in the egg nucleus and the polar bodies. However, multiple crossovers ... In theory, when the distance between a given locus and the centromere is maximum (that is, infinite), crossovers are so frequent that one may consider that alleles segregate independently. In this case, each offspring of a [ab] heterozygous mother producing [a1a2b1b2] 4n primary oocytes has a 1/3 probability of being homozygous [a1a2] or [b1b2]. For example, if the chromatid in the egg nucleus bears allele a1, there is 1 chance out of 3 that fusion will occur with a polar body possessing the allele a2 rather than b1 or b2. Of course, the same reasoning holds for the other alleles. Interestingly, this probability of transition to homozygosity is independent of the mode of fusion (terminal, central or random), as alleles segregate randomly from the primary oocyte to the polar bodies. Thus, effective recombination probability for any given locus is lower than the rate of crossover and, in theory, should never reach 1. Under automictic parthenogenesis with terminal, central or random fusion, extreme rate of crossover should result in alleles segregating independently. For these loci, the rate of transition to homozygosity is equal to the statistical probability of picking two identical items among two pairs without replacement, that is 1/3.

1. In the current ecological classification of termites, four feeding groups (I–IV) are recognised, corresponding to a gradient of decomposition from sound wood to highly mineralised organic matter in the soil. 2. Nitrogen stable isotopes (hereafter δ15N) were used to place termites from French Guiana rainforests along a wood-soil decomposition gradient, to test (i) whether feeding group assignation based on morphological characters was accurate and actually represented diet specialisation thresholds, and (ii) to what extent the dietary specialization of species is explained by phylogeny (phylogenetic autocorrelation). 3. δ15N values vary over a range of 13‰, suggesting that diet diversification contributes to the high species diversity in French Guiana. δ15N values span a similar interval in all Termitidae subfamilies. Ranges of different subfamilies broadly overlap, although each of them diversified preferentially on one side of the wood-soil decomposition gradient. Congeneric species share similar feeding habits, whereas distant species tend to feed on distinct substrates. 4. Feeding groups did not completely match stable isotope data: there was no discontinuity between Groups III and IV, and no correlation between anatomical criteria used to distinguish these groups and δ15N values. Nor was there any consistent difference in δ15N values between wood feeders of the families Rhinotermitidae (Group I) and Termitidae (Group II). We also suggest that species feeding outside the wood-soil gradient should be distinguished for their peculiar feeding requirements.

Premise of the study To characterize the level of genetic diversity and gene flow, as well as to identify unambiguously two African tropical tree species, Erythrophleum ivorense and E. suaveolens, we have developed a set of nuclear SSR (Simple Sequence Repeats) markers. Methods and Results Nine SSRs that display polymorphism in both species were identified. The nine newly developed SSR markers can be amplified in only two multiplexed reactions. Levels of polymorphism were assessed in two populations per species, yielding two to fifteen alleles per locus in E. ivorense and three to sixteen alleles per locus in E. suaveolens. Conclusions The SSR markers developed here are promising to study the spatial distribution of genetic diversity and the genetic delimitation of two Erythrophleum species from central Africa. © 2011 Botanical Society of America.

Premise of the study New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. Methods We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations. Results Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of S ã o Tom é, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogoou é River, suggesting refuges on both sides of the river bed. Conclusions The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity. © 2011 Botanical Society of America.

Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding.

International audience; Background and aims Species delimitation remains a difficult task in many groups of organisms. Even widespread and conspicuous tropical trees make no exception. Santiria trimera, an African rainforest tree, displays substantial morphological variability. While classical analysis of historical herbarium samples lead to the recognition of a single species, two morphotypes of S. trimera are regularly collected in Gabon and Equatorial Guinea, sometimes in sympatry: one form with stilt roots (SR) and another form without stilt roots (NSR). Methods To assess whether these forms constitute distinct taxa and to understand evolutionary processes within African Santiria, we combined a morphological and a spatial analysis of both sympatric morphotypes in northern Gabon with a phylogenetic analysis of samples from West and Central Africa, including the island of Sao Tome. Key results In Gabon, morphological traits, chloroplast DNA (cpDNA) and nuclear DNA (nuDNA) sequences congruently lead to the recognition of two well differentiated and reproductively isolated taxa corresponding to SR and NSR morphotypes. However, rare cases of the SR morphotype bearing DNA sequences typical of NSR individuals suggest that hybridization might sometimes occur. No evidence for habitat specialization of the two taxa was found. DNA sequences from Sao Tome formed monophyletic clades at both marker types and the nuDNA gene tree suggests that the Sao Tome population probably originated from Central Africa and subsequently underwent allopatric differentiation from continental populations. Conclusion In Central Africa, S. trimera is composed of at least two distinct sympatric species following the Biological Species Concept and calls for further morphological and phenological studies and experimental crosses between them to specify their taxonomic status. Our results also show that classical taxonomic species delimitation may not always be congruent with the Biological Species Concept, calling for more population-based in situ morphological and molecular genetic analyses.

International audience; 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.

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

International audience; In this study, we analysed spatial genetic structure (SGS) patterns and estimated dispersal distances in Milicia excelsa (Welw.) C.C. Berg (Moraceae), a threatened wind-pollinated dioecious African tree, with typically low density (approximately 10 adults/km(2)). Eight microsatellite markers were used to type 287 individuals in four Cameroonian populations characterized by different habitats and tree densities. Differentiation among populations was very low. Two populations in more open habitat did not display any correlation between genetic relatedness and spatial distance between individuals, whereas significant SGS was detected in two populations situated under continuous forest cover. SGS was weak with a maximum S(p)-statistic of 0.006, a value in the lower quartile of SGS estimates for trees in the literature. Using a stepwise approach with Bayesian clustering methods, we demonstrated that SGS resulted from isolation by distance and not colonization by different gene pools. Indirect estimates of gene dispersal distances ranged from sigma(g) = 1 to 7.1 km, one order of magnitude higher than most estimates found in the literature for tropical tree species. This result can largely be explained by life-history traits of the species. Milicia excelsa exhibits a potentially wide-ranging wind-mediated pollen dispersal mechanism as well as very efficient seed dispersal mediated by large frugivorous bats. Estimations of gene flow suggested no major risk of inbreeding because of reduction in population density by exploitation. Different strategy of seed collection may be required for reforestation programmes among populations with different extent of SGS.

Background: Understanding the mechanisms that control species genetic structure has always been a major objective in evolutionary studies. The association between genetic structure and species attributes has received special attention. As species attributes are highly taxonomically constrained, phylogenetically controlled methods are necessary to infer causal relationships. In plants, a previous study controlling for phylogenetic signal has demonstrated that Wright's F-ST, a measure of genetic differentiation among populations, is best predicted by the mating system (outcrossing, mixed-mating or selfing) and that plant traits such as perenniality and growth form have only an indirect influence on F-ST via their association with the mating system. The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift. The association of biparental inbreeding and inbreeding depression with population genetic structure, mating system and plant traits are also investigated. Results: Based on data from 263 plant species for which estimates of F-ST, inbreeding (F-IS) and outcrossing rate (t(m)) are available, we confirm that mating system is the main influencing factor of F-ST. Moreover, using an alternative measure of F-ST unaffected by the impact of inbreeding on effective population size, we show that the influence of tm on F-ST is due to its impact on gene flow (reduced pollen flow under selfing) and on genetic drift (higher drift under selfing due to inbreeding). Plant traits, in particular perenniality, influence F-ST mostly via their effect on the mating system but also via their association with the magnitude of selection against inbred individuals: the mean inbreeding depression increases from short-lived herbaceous to long-lived herbaceous and then to woody species. The influence of perenniality on mating system does not seem to be related to differences in stature, as proposed earlier, but rather to differences in generation time. Conclusion: Plant traits correlated with generation time affect both inbreeding depression and mating system. These in turn modify genetic drift and gene flow and ultimately genetic structure., SCOPUS: ar.j, info:eu-repo/semantics/published

Under the isolation-by-distance model, the strength of spatial genetic structure (SGS) depends on seed and pollen dispersal and genetic drift, which in turn depends on local demographic structure. SGS can also be influenced by historical events such as admixture of differentiated gene pools. We analysed the fine-scale SGS in six populations of a pioneer tree species endemic to Central Africa, Aucoumea klaineana. To infer the impacts of limited gene dispersal, population history and habitat fragmentation on isolation by distance, we followed a stepwise approach consisting of a Bayesian clustering method to detect differentiated gene pools followed by the analysis of kinship-distance curves. Interestingly, despite considerable variation in density, the five populations situated under continuous forest cover displayed very similar extent of SGS. This is likely due to an increase in dispersal distance with decreased tree density. Admixture between two gene pools was detected in one of these five populations creating a distinctive pattern of SGS. In the last population sampled in open habitat, the genetic diversity was in the same range as in the other populations despite a recent habitat fragmentation. This result may due to the increase of gene dispersal compensating the effect of the disturbance as suggested by the reduced extent of SGS estimated in this population. Thus, in A. klaineana, the balance between drift and dispersal may facilitate the maintenance of genetic diversity. Finally, from the strength of the SGS and population density, an indirect estimate of gene dispersal distances was obtained for one site: the quadratic mean parent-offspring distance, sigma(g), ranged between 210 m and 570 m.