Barbara Vinceti

Towards decoding the conifer giga-genome.

Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world’s conifer forests.

Climate change and tree genetic resource management: maintaining and enhancing the productivity and value of smallholder tropical agroforestry landscapes. A review

Anthropogenic climate change has significant consequences for the sustainability and productivity of agroforestry ecosystems upon which millions of smallholders in the tropics depend and that provide valuable global services. We here consider the current state of knowledge of the impacts of climate change on tree genetic resources and implications for action in a smallholder setting. Required measures to respond to change include: (1) the facilitated translocation of environmentally-matched germplasm across appropriate geographic scales, (2) the elevation of effective population sizes of tree stands through the promotion of pollinators and other farm management interventions; and (3) the use of a wider range of ‘plastic’ species and populations for planting. Key bottlenecks to response that are discussed here include limitations in the international exchange of tree seed and seedlings, and the absence of well-functioning delivery systems to provide smallholders with better-adapted planting material. Greater research on population-level environmental responses in indigenous tree species is important, and more studies of animal pollinators in farm landscapes are required. The development of well-functioning markets for new products that farmers can grow in order to mitigate and adapt to anthropogenic climate change must also consider genetic resource issues, as we describe.

Conservation Priorities for Prunus africana Defined with the Aid of Spatial Analysis of Genetic Data and Climatic Variables

Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites) from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1) was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2) at optimizing representativeness of the genetic diversity found throughout the species’ range. Populations in East African countries (especially Kenya and Tanzania) were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.

Spatially explicit multi-threat assessment of food tree species in Burkina Faso: A fine-scale approach

Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana) and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change). We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs), climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as ‘highly threatened’ due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted regeneration in the central part where the current threat level is high due to overexploitation. In the same way, population-specific recommendations can be derived from the individual and combined threat maps of the other 15 food tree species. The approach can be easily transferred to other countries and can be used to analyze general and species specific threats at finer and more local as well as at broader (continental) scales in order to plan more selective and efficient conservation actions in time. The concept can be applied anywhere as long as appropriate spatial data are available as well as knowledgeable experts.

Encuesta sobre la conservación y el uso de los recursos genéticos forestales en América Latina

Survey on the conservation and use of forest genetic resources in Latin America In order to understand the state of conservation and use of forest genetic resources in Latin America, an on-line survey of forestry personnel and organizations was conducted in 2006. Most respondents work on forestry, agroforestry and human-resource development, at national government organizations and universities. Research is local and focuses on developing agroforestry systems and on production and propagation trials. The top problems identified are the lack of funds, policies and recognition of the importance of forest genetic resources. According to the respondents, it is necessary to set priorities for work, define species of common interest, and work collaboratively to optimize resources. Professionals also lack information resources and mechanisms to communicate with peers, and recommended the creation of a regional network of specialists.

Phylogeography of African Locust Bean (Parkia biglobosa) Reveals Genetic Divergence and Spatially Structured Populations in West and Central Africa

Abstract The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modeled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using 8 nuclear microsatellites. Individual-based assignments clearly distinguished 3 genetic clusters, extreme West Africa (EWA), center of West Africa (CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (allelic richness after rarefaction [AR] = 6.4, expected heterozygosity [HE] = 0.78, and observed heterozygosity [HO] = 0.7) and CA (AR = 5.9, HE = 0.67, and HO = 0.61) compared with populations in CWA (AR = 7.3, HE = 0.79, and HO = 0.75). The overall population differentiation was found to be moderate (FST = 0.09). A highly significant isolation by distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modeling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory approximate Bayesian computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160000 years before present (BP), then a second split divided CA and CWA, about 100000 years BP. However, our genetic data do not enable us to conclusively distinguish among a few alternative possible scenarios.

Exploring local knowledge and preferences for shea (Vitellaria paradoxa) ethnovarieties in Southwest Burkina Faso through a gender and ethnic lens

Abstract In Africa’s ‘shea belt’, the shea tree (Vitellaria paradoxa) plays a central role in rural livelihoods and ecosystems. Yet, it faces many threats. The aim of this study is to examine local people’s classification systems and preferences for shea ethnovarieties in Burkina Faso to support domestication efforts that respect local priorities. Work was carried out among the Bobo, Sambla, Mosse and FulBe ethnic groups in two villages in south-west Burkina Faso. Participatory characterization and ranking matrices were used with 10 groups segregated by gender and ethnicity to understand if knowledge and preferences for shea ethnovarieties vary between gender and ethnic groups. Results show a general agreement across groups about top-cited ethnovariety names, characteristics and key criteria defining the classification system. Participants identified a total of 25 shea ethnovarieties according to 11 primary fruit and nut variants. The number of ethnovarieties cited varied slightly across groups, with greater consistency across ethnicities than across gender groups. Each ethnic and gender group identified certain ethnovarieties not cited by their ethnic or gender counterparts. Two ethnovarieties – ‘small shea fruit’ and ‘big shea fruit’ – were preferred across groups. The study highlights the value of gender-sensitive participatory research for understanding local botanical knowledge and preferences.