Rapid progress is being made in many areas of forest population genetics owing to the newly available molecular techniques and the fast growth of genomic and sequence data. This paper reviews the currently available genetic markers and their applications in studies on gene diversity, population structure and differentiation, gene flow, introgression, phylogeny and gene evolution. Various marker-based population analyses have highlighted the evolutionary history of many tree species. However, up to now, genetic markers have not fulfilled the expectations for studies on the adaptive variation and the effects of natural selection on forest tree populations. Studies based on integrated and extensive genome sampling, especially the coding regions of the genome, in combination with adaptive traits can potentially improve this situation. This would provide us with a comprehensive knowledge of the evolutionary mechanisms shaping the population changes, both adaptive and neutral.
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