Faculty of Agricultural and Applied Biological Sciences, Ghent University, 9000 Gent, BELGIUM.
Plant genetic resources (PGR), i.e. inter- and intra-specific plant diversity for current and future human use- are vital for the survival and well-being of humanity. However, the economic plant diversity and its conservation status in natural stands, managed ecosystems, farmers' fileds, home gardens and in other in situ settings is often poorly understood and regarded as seriously threatened by human disturbance. There is therefore an increasing recognition of the necessity to assess and optimize conservation actions and link these effectively with ex situ preservation approaches. Geographic Information Systems (GIS) and ecogeographic analysis could contribute significantly to improved understanding and monitoring of spatial and temporal patterns of biodiversity to support conservation actions of plant species. The hypothesis tested in this dissertation is the following: geospatial analysis of plant diversity and distribution can clearly detect geographic inter-specific and intra-specific diversity and distribution patterns, which allows prioritizing those plant species populations or distribution areas that should be considered for in situ conservation and germplasm collecting. This proposition is tested by (1) mapping plant diversity and distribution in several plant genetic resources case studies; and (2) by soliciting experts' feedback on the modelling of species' distributions. Their responses allow to better understanding of how useful such analyses can be in supporting local practitioners in the implementation of conservation measures.
The first part of this work presents an overview of those relevant techniques and advances in ecogeographic studies of PGR that can be used to analyse biodiversity data on the basis of field-collected data and to target further germplasm collecting for ex situ conservation. First of all, some important general considerations are articulated for setting up new research projects that are aimed at assessing the conservation status of PGR and/or monitoring trends in (economic) plant diversity on the basis of ecogeographic data. A brief introduction to commonly used methods and techniques for the analysis of inter- and intra-specific diversity is provided. The latter include multivariate methods such as clustering and ordination. Several techniques to map (economic) plant diversity data are discussed and ways to check and improve data quality are explained. Finally a synopsis of methods for Environmental Envelope Modelling (EEM- see below) and an overview of useful open-access and commercial statistical and GIS packages is presented.
Special emphasis is given to molecular marker concepts and examples of their application as well as geospatial analysis to carry out diversity analysis and optimize in situ conservation. Recent development of new powerful molecular tools that reveal many genome-wide polymorphisms has created novel opportunities for assessing genetic diversity, especially when these markers can be linked to key adaptive traits and are employed in combination with new geospatial methods of geographic and environmental analysis. New methods to prioritize varieties, populations and geographic areas for in situ conservation, and to enable monitoring of genetic diversity over time and space, are now available to support in situ germplasm management of crop and tree genetic resources.
For most plant species in the tropics and subtropics, including many crop wild relatives and socio-economically important tree species, only a limited amount of information on their natural distribution is currently available. EEM is considered a useful tool for providing vital missing information on the natural distribution of a species. Nevertheless, application of EEM for conservation planning requires careful validation. Opinions of experts who have worked in the field on conservation, seed collection and ecology of the specific species of interest offer a valuable and independent information source to validate EEM, because of their first-hand experience with species occurrence and absence. However, their use in model validation has always remained limited due to the subjectivity of their feedback. In this thesis, cultural consensus theory is utilized to formalize expert model evaluations. Such approaches allow a wider use of this information in model validation and improvement, and complement conventional validation methods of presence-only modelling. Online GIS and survey applications facilitate expert consultation.
The concepts and methods described above are applied in three case studies to demonstrate their usefulness for PGR in situ conservation and germplasm collecting: (1) an assessment of the diversity and conservation status of potato wild relatives endemic to Bolivia; (2) a review of peach palm (Bactris gasipaes Kunth) diversity, distribution, and PGR management; and (3) mapping molecular intra-specific diversity of cherimoya (Annona cherimola Mill.).
Bolivia is a centre of wild relative diversity for several crops, among them potato, which is a globally significant staple and the principle food crop in this country. Despite their relevance for plant breeding, limited knowledge exists about their in situ conservation status. GIS and distribution modelling with the software Maxent are applied to better understand geographic patterns of endemic wild potato diversity in Bolivia. In combination with threat layers, the conservation status of all endemic species, 21 in total, is assessed. Following the International Union for Conservation of Nature (IUCN) Red List ecogeographic criteria area of occupancy and extent of occurrence, at least 71 % (15 of 21 species) has a preliminary vulnerable status or worse. Our results show that five of these species require special conservation attention because they are highly threatened by increased accessibility of areas for human disturbances, fires and livestock activities pressure leading to overgrazing. Highest species richness occurs in south-central Bolivia, in the departments Santa Cruz and Chuquisaca. However, this area is severely threatened by the menaces mentioned above. The costs to implement conservation measures at these locations may be too high compared to other areas. Therefore a prioritization exercise, excluding 25 % of the most-threatened occurrence sites, is carried out identifying the most species rich area and complementary areas. The first priority area for in situ conservation according to our reserve selection exercise is central Bolivia, Cochabamba, which is less threatened than the potato wild relatives’ hotspot in south-central Bolivia. Only seven of the 21 species have been observed in protected areas. Understanding of the coverage of potato wild relatives' distribution in the protected areas can be improved by starting inventories in parks and reserves with high levels of modelled diversity. Finally, five of the 21 are either not conserved in one or more genebanks across the world or are conserved with less than five accessions, i.e. samples of living plant material collected from particular locations. New materials of these species should be included in genebanks to improve ex situ conservation of the potato gene pool.
Peach palm (Bactris gasipaes Kunth) is a multi-purpose palm tree that produces starchy, edible fruits and palm hearts. It may be considered the most economically important domesticated palm species of the Neotropics and has been widely used since early pre-Columbian times. Wild and cultivated peach palm populations are genetically diverse and could offer useful traits for breeding. Changes in land use and climate change pose a serious threat to wild populations in situ. While several large ex situ field collections of cultivated peach palm accessions exist, these are increasingly difficult to maintain because of the high costs. Screening peach palm diversity for biochemical and morphological traits of commercial and nutritional value would provide a basis for rationalizing collections and enhance future use of peach palm genetic resources. Indeed, well-chosen elite material could then be used either directly for production, or in breeding to develop improved peach palm varieties. At the same time, better propagation techniques should be developed to ensure wide distribution of elite peach palm clonal material.
A case study with cherimoya (Annona cherimola Mill.) in its Andean distribution range, explores the possibilities of incorporating molecular marker characterization data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, Cherimoya is a Neotropical fruit tree species. Its fruits are widely praised for their excellent taste and smell. The species is therefore considered to have high potential for commercial production and income generation for both small and large-scale producers in subtropical climates. Spatial analyses are utilized to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru characterized with microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. High levels of allelic richness and locally common alleles are evidenced in cherimoya's putative centre of origin, southern Ecuador and northern Peru. This suggests accumulated genetic resources resulting from a long history of human management and adaptation of trees to local climate conditions. Therefor these areas should be prioritized for in situ conservation. Levels of diversity in southern Peru and especially in Bolivia are significantly lower. However, the tree stands in these areas belong to a genetically different population than those in southern Ecuador and northern Peru. They may contain genetic resources that are not present in the above-mentioned centres of diversity. It is therefore important to consider these areas too in defining conservation strategies.
The results obtained in the different case studies support the hypothesis of this dissertation as stated above, i.e. that geospatial analysis of plant diversity and distribution analysis can clearly detect geographic inter-specific and intra-specific diversity patterns, which allows more effective prioritization of those plant species populations and distribution areas to be considered for in situ conservation and germplasm collecting.
First, the results from the expert validation exercise of EEM show that many professionals are fairly positive about the use of distribution modelling for in situ conservation planning. This suggests that such analysis can support local professionals in their planning work of managing and conserving plant genetic resources. However, these tools have limitations in their precision. Consequently their applicability to support conservation actions in the field remains restricted. Further improvement of distribution modelling techniques to provide support for more local conditions would therefore be helpful. A key point is to increase the availability of more detailed geospatial environmental layers.
Many professionals working with plant genetic resources and/or in the field of economic botany may opt to apply themselves geospatial analysis but do not necessarily have the required experience. In parallel with the research for this thesis, a manual on plant diversity and distribution has been developed. This manual responds to the increasing demand from professionals working with plant genetic resources such as botanists, agronomists and ecologists for this type of analyses.
Secondly, in the case studies of mapping wild potatoes and cherimoya diversity clear and detailed geographic patterns of respectively taxonomic and molecular diversity could be detected. This suggests that diversity mapping allows more effective prioritizing of areas for conservation and germplasm collecting at both inter- and intra-specific levels. On the contrary, the peach palm review of existing genetic studies did not provide evidence for areas of high diversity of this particular species. Studies from existing literature included often only a limited number of populations and used different sampling methods and marker types. This makes it difficult to carry out meta-analysis. Therefore standardization of methods and range-wide analysis across species distributions are recommended for better detection of genetic diversity hotspots of plant species. Range-wide analyses of species genetic diversity become increasingly feasible as the cost of diversity studies with molecular markers becomes cheaper.
Such analyses can also be applied to other plant species. This has been done now for example in a distribution and conservation assessment of 100 tree species native to Latin America and the Caribbean named MAPFORGEN (www.mapforgen.org).
Several models and scenarios are discussed that can explain the diversity patterns that are observed in the wild potato and cherimoya studies. The drivers that shape the geographic patterns of diversity in these two case studies are completely different. The occurrence and evolution of potato wild relatives have been shaped by natural processes over hundreds, thousands and millions of years. The distribution of cherimoya genetic diversity follows a pattern of human-mediated crop dispersal that started after about 13,000 years ago when agriculture originated in different parts of the world during the Neolithic revolution.
Future challenges are being discussed including approaches and concepts of data sharing and standardization. The latter would make it possible to combine plant diversity datasets leading to stronger analyses to detect geographic patterns of plant diversity and distribution. Standardization of passport data, characterization and evaluation also enhance comparability of study results in meta-analyses. There is also an increasing need to learn more about phenotypic variation in adaptive characteristics and other functional traits of plant species to identify materials with traits of interest; to understand the responses of plant species to climate change; and to estimate the evolutionary potential of populations, to name a few. However phenotypic evaluation is costly. Smart approaches such as pre-selection of plant materials and populations by means of molecular characterization are required to optimize evaluation of functional genetic variation. The potential and limitations of using molecular characterization and citizen science in monitoring economic plant diversity are discussed. The thesis ends with reflections on possible environmental and cultural factors that influence maintenance, reduction or increase in cultivated plant diversity. A better understanding of these drivers helps to decide which interventions are necessary to enhance use and conservation of PGR under specific cultural, socio-economic, and biophysical conditions.