Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure

<p>Abstract</p> <p>Background</p> <p>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 <it>F</it>_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 <it>F</it>_STvia 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.</p> <p>Results</p> <p>Based on data from 263 plant species for which estimates of <it>F</it>_ST, inbreeding (<it>F</it>_IS) and outcrossing rate (<it>t</it>_m) are available, we confirm that mating system is the main influencing factor of <it>F</it>_ST. Moreover, using an alternative measure of <it>F</it>_STunaffected by the impact of inbreeding on effective population size, we show that the influence of <it>t</it>_mon <it>F</it>_STis 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 <it>F</it>_STmostly 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.</p> <p>Conclusion</p> <p>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.</p

Can seed exchange networks explain the morphological and genetic diversity in perennial crop species? The case of the tropical fruit tree Dacryodes edulis in rural and urban Cameroon

Crop seed exchange networks, shaped by social dynamics, strongly influence the organization and breadth of plant diversity in human-managed environments. Integrating an urban and market perspective, this study explores the diversity dynamics of a socio-economically important Central African fruit tree species, the African plum tree. Tree owners in urban, peri-urban and rural sites use seeds from different origins as their main propagation material, leading to locational variations in genetic diversity and structure. This analysis contributes toward building a framework to inform the research agenda of cultivated African fruit trees, by highlighting the important role of urban centers in safeguarding crop genetic resources

Untangling Biocultural and Socioeconomical Drivers of African Plum Tree (Dacryodes edulis) Local Nomenclature Along a Rural-Urban Gradient in Central Cameroon

In Cameroon, the African plum tree (Dacryodes edulis [G. Don] H. J. Lam) is widely cultivated for its fruits, which contribute significantly to household food security and economy. In order to analyze the links between the social and ecological systems that result in the remarkable fruit diversity, we focused on how the important varietal diversity of African plums was perceived and named by tree owners. We conducted semi‑structured interviews in Center-Cameroon with 142 people belonging to the Beti ethnic group, in urban (Yaoundé), peri-urban and rural areas, and analyzed the data qualitatively and quantitatively. Along this urbanization gradient linking production to consumption regions, 158 different translated names were recorded. Most names (80%) were cited once, but some names based on fruit size and taste were common across the gradient. Although the highest total number of names was recorded in the rural site, many different names were also found along the urban–rural gradient. We did not detect difference in the number of named African plums between respondents with different characteristics. The local classification of African plums among the Beti was structured predominantly according to morphological and organoleptic criteria, but also to symbolic and practical criteria. African plums’ names were based on people’s fruit preferences, that favor large, oily, and blue to black fruits, and disregard pink-colored watery plums. This study is an entry point to explore the rising trade and thus ongoing domestication of the African plum tree from an often neglected perspective, that of local nomenclature

New microsatellite markers for Dacryodes edulis (Burseraceae), an indigenous fruit tree species from Central Africa

Microsatellites were designed and characterized in the African fruit tree species Dacryodes edulis (Burseraceae). The fruits are commercialized throughout Central Africa and the species is present in forested environments as well as cultivated systems. The high variability of these markers makes them suitable to investigate the structure of genetic diversity in this important food tree species from Central Africa. From a genomic library obtained by next-generation sequencing, 21 new polymorphic microsatellite loci were developed. Tested on 95 individuals from four populations coming from three countries of the Congo Basin, the microsatellites displayed two to 20 alleles (mean 7.5; expected heterozygosity 0.003 to 0.937, mean 0.666). The transferability of microsatellites was effective for four other Dacryodes species (D. buettneri, D. igaganga, D. osika, D. pubescens). This set of newly developed microsatellite markers will be useful for assessing the genetic diversity and differentiation as well as gene flow patterns of D. edulis in tropical forests from Central Africa

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Background: 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. Methodology/Principal Findings: We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. Conclusions/Significance: Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications