Population genetic analysis and evolutionary history of the pine needle pathogen, Dothistroma pini

Abstract

Dothistroma needle blight (DNB) is a pine needle disease that causes substantial economic damage in the timber industry worldwide, costing millions in capital each year. The disease has a global distribution, being able to tolerate a variety of different climates and environmental conditions. Early symptoms of the disease include yellow discolouration, and, as the disease progresses, distinctive red spots or banding can be observed. Ultimately, photosynthesis is halted, causing the needles to become necrotic, the fruiting bodies erupt through the epidermis and the needles are prematurely cast, leading to reduced tree growth. In extreme cases of the disease, tree death has been observed. DNB is caused by two fungal pathogens, Dothistroma septosporum, which has a global distribution, and D. pini, which is limited to the Northern Hemisphere. Numerous studies have been conducted on D. septosporum, where its global distribution, population structure, genetic diversity and introduction pathways have been identified. In contrast, such knowledge about D. pini remains limited, where only two studies have been published that investigated the population genetics of this pathogen in parts of Europe. In this dissertation, I therefore aim to close this knowledge gap by investigating the population genetics and movement of D. pini in the Northern Hemisphere. The dissertation includes three chapters: a literature review and two independent research chapters. The chapters in this dissertation are written in typical journal style. Currently, the most common tools used in population- and evolutionary studies are genomic markers, specifically single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Thus, the first chapter of this dissertation presents a review of the literature on these two genomic markers and how they can be used to trace the global migration and evolutionary patterns of forest pathogens. The review includes a comparison of SNPs and STRs as well as discussions on where these markers are found in a genome and how they can be identified. The different modes of migration that a pathogen can follow are also discussed. Furthermore, different bioinformatic software that can be used to infer pathways of pread of a pathogen are provided, discussed and compared. Some examples are provided that illustrate the usefulness of genomic markers to infer migration patterns and introduction pathways of forest pathogens. A previous study on D. pini included populations from 12 countries in Europe. Population genetic analyses were conducted to determine the genetic diversity and population structure of the pathogen on this continent. The country that presented the highest level of genetic diversity and evidence of sexual reproduction was France, but the study only considered strains from central France. Recently, D. pini isolates from the southern parts of France became available, which begged the question of how they relate to the central France population. Thus, the second chapter of this dissertation focuses on the population dynamic of D. pini in France. The aim of this chapter was to determine whether the populations from central- and southern France are genetically related or if they were introduced into France independently. Microsatellite markers were used to investigate the southern France isolates, and this data, combined with the data available from central France, were used for downstream population genetic analyses.

Even though D. pini populations have been investigated in Europe, no knowledge is available regarding the population structure and diversity of the pathogen in the USA as well as and how these populations compare across continents. Thus, the aim of the third chapter was to investigate the global genetic diversity and population structure of D. pini as well as to determine the direction of pathogen movement between Europe and the USA. A global D. pini dataset was compiled by obtaining the European microsatellite data from the study by van der Nest et al. (2023), by including the microsatellite data from Chapter 2 of this dissertation, and by completing and including an existing, unpublished USA dataset. The bioinformatic programme DIYABC was used to determine the migration pattern of D. pini.

This body of work presents the most complete population study of D. pini to date, where the research outcomes highlight what the global population dynamic of the pathogen is, as well as its migration patterns. Dothistroma pini continues to spread and threaten the forestry industry and it might just be a matter of time before the pathogen is introduced into the Southern Hemisphere, where currently it remains absent. Knowledge of such pathways and migration patterns can ultimately help formulate useful protocols to prevent the further spread and intercontinental movement of D. pini.