Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed which predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival or reproduction. Here, we examine the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple paired urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations and genomic variation was best explained by geographic distance rather than environmental factors. Moreover, both urban and forest populations appear to have undergone population declines which are coincident with extensive human-activity around the Panama Canal during the last few centuries rather than recent urbanisation. Overall, our study underscores the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales. Failure to take this into account when interpreting comparisons between urban and non-urban areas may underestimate the impact of urbanisation.

The occurrence of alternative morphs within populations is common but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, whilst others (in particular, females) migrate to sea for a period of marine growth. Here we performed transcriptional profiling (“RNA-seq”) of the brain and liver of male and female brown trout to understand the genes and processes that differentiate migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with greater number of genes expressed differentially in the liver (n = 867 genes) compared to the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 18) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life-histories within and between the sexes, and point towards a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.