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Introduction
Diplodia pinea (Desm.) Kickx (=Sphaeropsis sapinea (Fr.:Fr.) Dyko& Sutton) is an opportunistic, latent endophytic pathogen of Pinus spp. and other conifers. The fungus was identified for the first time in France on dead P. sylvestris needles as a saprophyte. Since that time, it has been reported from most parts of the world where pines and other coniferous trees are found (Swart et al. 1985; Stanosz et al. 1997; Burgess et al. 2004a). In contrast, the sibling species Diplodia scrobiculata (de Wet et al. 2003) has a limited distribution in native and nonnative ranges of pines. It is hypothesized that the movement of D. pinea around the world including the tropics and southern hemisphere has been the result of the movement of germplasm through human activities (Burgess and Wingfield 2002).
Population genetics
Intensive management of agricultural and forestry ecosystems affect the micro-organisms that occur in these environment systems. Strong selective pressures are placed on micro-organisms, many of which are pathogens, to adapt to the changing and specific conditions that are imparted by various agronomic and management protocols (McDonald and McDermott 1993; Milgroom and Fry 1997; McDonald 1997; Linde 2010). The impacts of these changes are difficult to measure and predicting what control measures will be needed to contain these altered populations is complex.Knowledge about the population dynamics, including diversity, mating systems and modes of spread.
DNA sequences
Variation in DNA sequences can be used to detect genetic variation within species via amplifying several genomic regions that have polymorphisms (Taylor et al. 2006; Torriani et al. 2008). DNA sequence data from different genomic loci of D. pinea were not only useful to differentiate the fungus based on phylogeny from other Diplodia sp and morphotypes, but have also been indirectly used to analyze diversity of genotypes. For example, analysis of ITS region sequences showed that D. scrobiculata from Mexico is more diverse than D. pinea from South Africa and Indonesia (De Wet et al. 2000). The same pattern was observed for DNA sequence data of protein coding genes (BT2, CHS, EF-1α, ACT, CAL and GPD)
Isozymes
Isozymes are molecular forms of an enzyme, which usually have similar enzymatic properties, but different amino acid sequences (Weeden and Wendel 1989; Bonde et al. 1993). They are highly polymorphic between species and to a lesser extent within species (Glynn and Reid 1969).
Chapter One: Biology and genetic diversity of the latent pathogens of Pine, Diplodia pinea and D. scrobiculata
Chapter Two: Distribution of Diplodia pinea and its genotypic diversity within asymptomatic Pinus patula trees
Chapter Three: Population genetic analysis of South African Diplodia pinea isolates reveals diverse sources of infection and cryptic recombination
Chapter Four: Diplodia scrobiculata found in the southern hemisphere
Chapter Five: High levels of genetic diversity and cryptic recombination are widespread in introduced Diplodia pinea populations
Chapter Six: Sources of Diplodia pinea endophytic infections in Pinus patula and P. radiata seedlings in South Africa Summary
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Understanding the global population genetics of Diplodia pinea and its life cycle in plantation pines
