Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution

Local adaptation emerges when a population has differentially evolved compared to other populations within a given species in response to particular selective pressures imposed by biotic or abiotic components of its local environment, resulting in a higher fitness of this focal population in its environment compared to other members of the same species and/or compared to other environments (Williams 1966; Kaltz & Shykoff 1998). Local adaptation is an ideal situation for studying the mechanisms of evolution and adaptation, as one can compare different populations belonging to the same species with negligible differentiation beyond the traits or genes involved in adaptation. Patterns and mechanisms of local adaptation are still less studied in ‘microbes’, that is, micro-organisms such as fungi, bacteria, than in plants and animals, mostly because they are less conspicuous or charismatic, and were long thought to display little differentiation among populations because of their high dispersal abilities (Taylor et al. 2006). Yet, they are good models for studying patterns and processes of adaptation. They are indeed tractable for experiments, in particular for experimental evolution experiments thanks to short generation times, and for genetic and genomic studies, thanks to an often easy access to the haploid phase and their small genomes (Gladieux et al. 2014; Croll & McDonald 2017). Their lifestyle often involving symbiosis, either mutualistic or pathogenic, is also an interesting feature for the study of adaptation, as this can lead to co-evolution and/or host specialization. Furthermore, microbes can be parasitized, such as in the case of phages parasitizing bacteria or viruses parasitizing fungi. Abiotic selective pressures, such as temperature or pesticides, can also lead to local adaptation in bacteria and fungi (Branco et al. 2017; Mboup et al. 2012; Delmas et al. 2017; Walker et al. 2017). We can also expect interactions between biotic and abiotic factors, with for instance host local adaptation of a microbe mediated by temperature or the presence of its parasite (Laine 2008; Meaden & Koskella 2017). Furthermore, adaptation in microbes is essential to study because these organisms have great impact on ecosystem functioning as well as on human health and food security. Many microbes are human pathogens or infect crops or livestock (Fisher et al. 2012; Gladieux et al. 2015). Many other microbes have been domesticated for food maturation (Gladieux et al. 2014; Dequin et al. 2017). Adaptation in microbial pathogens can involve evolution of fungicide resistance or adaptation to host resistance, which has considerable impact on disease epidemics (Croll & McDonald 2017). This Molecular Ecology Special Issue on ‘Microbial Local Adaptation’ highlights different approaches that can be used to study patterns and mechanisms of adaptation in microbes, and this special issue compiles studies reporting evidence of local adaptation in natural populations, studies using experimental evolution for elucidating how selection can produce adaptation or what constraints exist that prevent optimal adaptation, and studies detecting footprints of adaptation in genomes and identifying the genetic basis of adaptation. Biological models in this special issue include viruses, bacteria, oomycetes and fungi, most of which are plant or animal (including human) pathogens, and some domesticated fungi (wine yeasts). Some papers in the present issue review the literature on a particular aspect of local adaptation, for instance on the genetic basis of local adaptation in crop pathogens or on insights obtained from experimental evolutionary studies of local adaptation in plant viruses or on trade-offs (Bono et al. 2017; Croll & McDonald 2017; Elena 2017).