Speciation with gene flow in an island endemic hummingbird

We examined speciation in streamertail hummingbirds (<i>Trochilus polytmus</i> and <i>Trochilus scitulus</i>), Jamaican endemic taxa that challenge the rule that bird speciation cannot progress in situ on small islands. Our analysis shows that divergent selection acting on male bill color, a sexual ornament that is red in <i>polytmus</i> and black in <i>scitulus</i>, acts as a key reproductive barrier. We conducted a population-level analysis of genomic and phenotypic patterns to determine the traits that contribute the most to speciation despite ongoing gene flow across a narrow hybrid zone. We characterized genomic patterns using 6,451 single-nucleotide polymorphisms and a segment of the mitochondrial control region. Our analyses revealed high diversity within species, and low divergence between them, consistent with a recent speciation event or extensive gene flow following secondary contact. We observed narrow clines in two phenotypic traits and several SNP loci. The cline width for male bill color is only 2.3 km, marking it as one of the narrowest phenotypic clines documented in an avian hybrid zone. The coincidence of estimated cline centers with the Rio Grande Valley suggests that this landscape feature may contribute to hybrid zone stability. However, given that streamertails are highly mobile, it is unlikely that such a narrow river acts as a physical barrier to dispersal. The limited genomic divergence across scanned regions of the genome offers little support for postmating reproductive barriers. Instead, our findings point to strong premating selection acting on bill color as the primary driver of streamertail speciation.