Microsatellites in the tree Foetidia mauritiana (Lecythidaceae) and utility in other Foetidia taxa from the Mascarene Islands.

PREMISE OF THE STUDY: Polymorphic markers were required for a native tree of the Mascarene Islands, Foetidia mauritiana (Lecythidaceae), to investigate the effects of fragmentation of lowland tropical habitats on tree mating systems and on gene flow. METHODS AND RESULTS: Using microsatellite enrichment and next-generation sequencing, we identified 13 microsatellite loci (dinucleotide repeats). They were highly polymorphic in 121 trees sampled in the largest three populations on Réunion, revealing 2-17 different alleles per locus. Furthermore, they were found to be polymorphic in conspecific populations on Mauritius and in F. rodriguesiana from Rodrigues. CONCLUSIONS: These results indicate the utility of these markers to investigate genetic diversity, mating systems, and gene flow in a genus native to the biodiversity hotspot of Madagascar and the Indian Ocean islands.

Isolation and Characterization of Microsatellite Markers for Mimusops balata (Sapotaceae) and Cross-Amplification in Other Mimusops Species.

Mimusops balata (Sapotaceae) is an endemic tree species from La Réunion and Mauritius. Like many species growing in lowland forests in La Réunion, it has suffered from human disturbances. We developed twelve microsatellite markers for M. balata and tested cross-amplification in five other Mimusops species to have powerful tools for genetic diversity studies. Genotyping peaks were of very low quality for two loci and were consequently abandoned for the genetic diversity analyses. Ten microsatellite loci were tested on 34 individuals of M. balata from two natural populations. The number of alleles per locus ranged from one to seven. The observed and expected heterozygosity levels varied from 0.000 to 0.823, and from 0.000 to 0.812 respectively. Two loci deviated from the Hardy-Weinberg equilibrium. The presence of null alleles was detected for one of these two loci. Nine to ten loci cross-amplified reliably in Mauritian species, for the other three species, four to six loci show successful amplifications. These polymorphic microsatellite markers are now available for population genetic investigations in Mimusops species aiming to establish accurate guidelines for conservation managers.

Polymorphic microsatellite loci from Dacryodes edulis (Burseraceae), a Central African rainforest and fruit-tree species.

PREMISE OF THE STUDY: Microsatellite markers were isolated and characterized from Dacryodes edulis (Burseraceae), a tropical rainforests fruit tree of central Africa. METHODS AND RESULTS: Using an enrichment protocol, six microsatellites loci were developed from Dacryodes edulis. We investigated polymorphism using 45 trees from three widely separated populations in Cameroon. All loci were polymorphic, with the number of alleles ranging from 2 to 15. Polymorphism was widely variable among loci and expected heterozygosities ranged from 0.06 to 0.84 with a mean value of 0.49. CONCLUSIONS: These loci will be useful for the in-depth analysis of population structure and phylogeographic variation throughout the distribution range of Dacryodes edulis and other related taxa, Dacryodes buettneri and D. normandii, in which all loci were also amplified. Furthermore, they will offer the opportunity to study early domestication processes acting on the genetic diversity of Dacryodes edulis.

Insights into the biogeographical history of the Lower Guinea Forest Domain: evidence for the role of refugia in the intraspecific differentiation of Aucoumea klaineana.

Determining the biogeographical histories of rainforests is central to our understanding of the present distribution of tropical biodiversity. Ice age fragmentation of central African rainforests strongly influenced species distributions. Elevated areas characterized by higher species richness and endemism have been postulated to be Pleistocene forest refugia. However, it is often difficult to separate the effects of history and of present-day ecological conditions on diversity patterns at the interspecific level. Intraspecific genetic variation could yield new insights into history, because refugia hypotheses predict patterns not expected on the basis of contemporary environmental dynamics. Here, we test geographically explicit hypotheses of vicariance associated with the presence of putative refugia and provide clues about their location. We intensively sampled populations of Aucoumea klaineana, a forest tree sensitive to forest fragmentation, throughout its geographical range. Characterizing variation at 10 nuclear microsatellite loci, we were able to obtain phylogeographic data of unprecedented detail for this region. Using Bayesian clustering approaches, we demonstrated the presence of four differentiated genetic units. Their distribution matched that of forest refugia postulated from patterns of species richness and endemism. Our data also show differences in diversity dynamics at leading and trailing edges of the species' shifting distribution. Our results confirm predictions based on refugia hypotheses and cannot be explained on the basis of present-day ecological conditions.

Colonization processes and the maintenance of genetic diversity: insights from a pioneer rainforest tree, Aucoumea klaineana.

Despite recurrent episodes of range expansion and contraction, forest trees often harbour high genetic diversity. Studies of temperate forest trees suggest that prolonged juvenile phase and high pollen flow are the main factors limiting founder effects. Here, we studied the local colonization process of a pioneer rainforest tree in central Africa, Aucoumea klaineana. We identified 87% of parents among trees up to 20-25 years old and could thus compare direct parentage structure data with classical population genetics estimators. In this species, genetic diversity was maintained during colonization. The absence of founder effects was explained by (i) local random mating and (ii) local recruitment, as we showed that 75% of the trees in the close neighbourhood participated in the recruitment of new saplings. Long-distance pollen flow contributed little to genetic diversity: pollen and seed dispersal was mainly within stand (128 and 118 m, respectively). Spatial genetic structure was explained by aggregated seed dispersal rather than by mother-offspring proximity as assumed in classical isolation-by-distance models. Hence, A. klaineana presents a genetic diversity pattern typical of forest trees but does not follow the classical rules by which this diversity is generally achieved. We suggest that while high local genetic variability is of general importance to forest tree survival, the proximate mechanisms by which it is achieved may follow very different scenarios.

Small-scale spatial genetic structure in the Central African rainforest tree species Aucoumea klaineana: a stepwise approach to infer the impact of limited gene dispersal, population history and habitat fragmentation.

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.

Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species.

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.