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Despite the enormous advances in genetics, links between phenotypes and genotypes have been made for only a few nonmodel organisms. However, such links can be essential to understand mechanisms of ecological speciation. The Costa Rican endemic Mangrove Warbler subspecies provides an excellent subject to study differentiation with gene flow, as it is distributed along a strong precipitation gradient on the Pacific coast with no strong geographic barriers to isolate populations. Mangrove Warbler populations could be subject to divergent selection driven by precipitation, which influences soil salinity levels, which in turn influences forest structure and food resources. We used single nucleotide polymorphisms (SNPs) and morphological traits to examine the balance between neutral genetic and phenotypic divergence to determine whether selection has acted on traits and genes with functions related to specific environmental variables. We present evidence showing: (a) associations between environmental variables and SNPs, identifying candidate genes related to bill morphology (BMP) and osmoregulation, (b) absence of population genetic structure in neutrally evolving markers, (c) divergence in bill size across the precipitation gradient, and (d) strong phenotypic differentiation (P ST) which largely exceeds neutral genetic differentiation (F ST) in bill size. Our results indicate an important role for salinity, forest structure, and resource availability in maintaining phenotypic divergence of Mangrove Warblers through natural selection. Our findings add to the growing body of literature identifying the processes involved in phenotypic differentiation along environmental gradients in the face of gene flow.

Concern over rapid environmental shifts associated with climate change has led to a search for molecular markers of environmental tolerance. Climate-associated gene expression profiles exist for a number of systems, but have rarely been tied to fitness outcomes, especially in nonmodel organisms. We reciprocally transplanted corals between two backreef locations with more and less variable temperature regimes to disentangle effects of recent and native environment on survival and growth. Coral growth over 12 months was largely determined by local environment. Survival, however, was impacted by native environment; corals from the more variable environment had 22% higher survivorship. By contrast, corals native to the less variable environment had more variable survival. This might represent a "selective sieve" where poor survivors are filtered from the more stressful environment. We also find a potential fitness trade-off-corals with high survival under stressful conditions grew less in the more benign environment. Transcriptome samples taken a year before transplantation were used to examine gene expression patterns that predicted transplant survival and growth. Two separate clusters of coexpressed genes were predictive of survival in the two locations. Genes from these clusters are candidate biomarkers for predicting persistence of corals under future climate change scenarios.