Population genetics of plant parasitic nematodes.

There are increasing reports of damages caused by the stem and bulb nematode Ditylenchus dipsaci in the agri- and horticultural sector world-wide, most notably in the Netherlands, Germany, and Canada. Current management strategies are lacking, in large part due to the wide host range of D. dipsaci and the extreme variation in host preference encountered within the species. As a solution, researches have attempted to sub-divide the species into races which can be used to tailor management strategies. Up to now this has been done based off multiplication rates on specific hosts (i.e. differentials), but this was ultimately found to be infeasible. Furthermore, classification of samples based on host range is bound to misrepresent the diversity within plant parasitic nematode species as host compatibility is determined by a small number of genes. Therefore, to force a breakthrough in the classification of D. dipsaci, we think it is required to shift the paradigm away from host differential tests and towards methods that account for the full set of genomic features. To this end, the aim of this thesis is to establish a classification system for D. dipsaci that is based on the genetic similarity between isolates. To achieve this aim several questions need to be answered: 1) What is the extend of genetic diversity encountered within the species? 2) How many isolates need to be investigated for a reliable survey? 3) How to delineate genetic clusters such that they represent useful entities? The key to answering all these questions lies in understanding the population structure of D. dipsaci. However, this is complicated by several factors: The first being that important background information, such as the origin and the subsequent transmission routes of the species, are unknown. The second being that the obligate sexual mode of reproduction creates heterogeneous populations of genetically distinct individuals, which is not accounted for in existing sequencing analysis workflows. Because of these challenges, the analysis of D. dipsaci is supported with work on two better understood nematode species: Caenorhabditis elegans and Globodera pallida. These additional species help establish new methods and serve to identify common forces acting on nematode population structures.