Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Mammals are exposed to a diverse array of parasites and infectious diseases, many of which affect host survival and reproduction. Species that live in dense populations, large social groups, or with promiscuous mating systems may be especially vulnerable to infectious diseases owing to the close proximity and higher contact rates among individuals. We review the effects of host density and social contacts on parasite spread and the importance of promiscuity and mating structure for the spread and evolution of sexually transmitted diseases. Host social organization and mating system should influence not only parasite diversity and prevalence but may also determine the fitness advantages of different transmission strategies to parasites.