How rapidly can animal populations in the wild evolve when faced with sudden environmental shifts? Uplift during the 1964 Great Alaska Earthquake abruptly created freshwater ponds on multiple islands in Prince William Sound and the Gulf of Alaska. In the short time since the earthquake, the phenotypes of resident freshwater threespine stickleback fish on at least three of these islands have changed dramatically from their oceanic ancestors. To test the hypothesis that these freshwater populations were derived from oceanic ancestors only 50 y ago, we generated over 130,000 singlenucleotide polymorphism genotypes from more than 1,000 individuals using restriction site-associated DNA sequencing (RAD-seq). Population genomic analyses of these data support the hypothesis of recent and repeated, independent colonization of freshwater habitats by oceanic ancestors. We find evidence of recurrent gene flow between oceanic and freshwater ecotypes where they co-occur. Our data implicate natural selection in phenotypic diversification and support the hypothesis that the metapopulation organization of this species helps maintain a large pool of genetic variation that can be redeployed rapidly when oceanic stickleback colonize freshwater environments. We find that the freshwater populations, despite population genetic analyses clearly supporting their young age, have diverged phenotypically from oceanic ancestors to nearly the same extent as populations that were likely founded thousands of years ago. Our results support the intriguing hypothesis that most stickleback evolution in fresh water occurs within the first few decades after invasion of a novel environment. 27, 1964, the largest earthquake ever recorded in North America struck the south coast of Alaska (1, 2). This catastrophic event uplifted islands in Prince William Sound and the Gulf of Alaska in just a few minutes, creating ponds from formerly marine habitat and setting the stage for the diversification of threespine stickleback fish (Gasterosteus aculeatus) in these new freshwater sites. This seismic disturbance provides an excellent opportunity to address long-standing evolutionary questions regarding how often dramatic phenotypic shifts can happen over contemporary timescales (3-7).Despite examples of rapid divergence in wild populations, evolutionary rates may often be constrained by a suite of factors (8). For example, evolution in new habitats may be limited by waiting times for new beneficial mutations (9-11). Even when adaptation occurs from standing genetic variation, evolution via selection of numerous independent loci of small effect may be time consuming (12-16). We know, however, that evolution can occur rapidly, particularly under artificial selection or in human-altered landscapes (17-21). In addition, empirical studies in the wild-particularly in response to significant environmental changes-have demonstrated that strong selection and rapid evolution over decades may be more common than once thought (22-24).A rapid evolutionary response is predict...

Heterogeneous genetic divergence can accumulate across the genome when populations adapt to different habitats while still exchanging alleles. How long does diversification take and how much of the genome is affected? When divergence occurs in parallel from standing genetic variation, how often are the same haplotypes involved? We explore these questions using restriction site-associated DNA sequencing genotyping data and show that broad-scale genomic repatterning, fueled by copious standing variation, can emerge in just dozens of generations in replicate natural populations of threespine stickleback fish (). After the catastrophic 1964 Alaskan earthquake, marine stickleback colonized newly created ponds on seismically uplifted islands. We find that freshwater fish in these young ponds differ from their marine ancestors across the same genomic segments previously shown to have diverged in much older lake populations. Outside of these core divergent regions the genome shows no population structure across the ocean-freshwater divide, consistent with strong local selection acting in alternative environments on stickleback populations still connected by significant gene flow. Reinforcing this inference, a majority of divergent haplotypes that are at high frequency in ponds are detectable in the sea, even across great geographic distances. Building upon previous population genomics work in this model species, our data suggest that a long history of divergent selection and gene flow among stickleback populations in oceanic and freshwater habitats has maintained polymorphisms of alternatively adapted DNA sequences that facilitate parallel evolution.

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis.