Color polymorphism provides a tractable window into how selection, gene flow, and ecology interact to maintain phenotypic diversity and initiate divergence. I investigate the ecological and genomic bases of sympatric light and melanistic morphs in two reef hawkfishes,Paracirrhites arcatusandP. hemistictus, across Guam andHawai‘i. ForP. arcatusrevealed substantially lower density on Guam (0.086 ind/m²) than reported for Hawai‘i (0.292 ind/m²) and a strong skew away from the melanistic morph on Guam (7.0%) relative to Hawai‘i (39.6%), indicating geography-dependent morph structure and habitat context. Redundancy analysis showed that a simplified model explained slightly more variance than the model developed for the Hawaiian population, while multidimensional niche-overlap tests detected significant differentiation among morphs despite weak univariate habitat preferences. Whole-genome resequencing (148 genomes) recovered modest population differentiation (Guam-Hawai‘i mean FST= 0.0047) and slightly higher between-morph genome-wide FSTon Guam (0.0015) than Hawai‘i (0.0010). Sliding-window scans and SNP outlier tests identified numerous regions of elevated differentiation, including pigmentation genes (e.g.,gpnmb,sox9,sfxn1), supporting “islands of divergence” under gene flow. InP. hemistictus(69 genomes), morph divergence was markedly greater (mean FST= 0.0750), with spatial sorting across Orote Peninsula and selective signatures (e.g.,Chd1) pointing to more advanced separation without single diagnostic loci. Sympatric incipient divergence is supported inP. arcatus, particularly in Hawai‘i, while there is deeper genome-wide separation in the morphs ofP. hemistictus.Together, these results show that similar light/melanistic polymorphisms can follow distinct trajectories driven by ecological conditions and including competitive environments.
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