Urbanization alters ecosystems, fragmenting natural habitats, and hence, increasing isolation between populations. Therefore, a reduction in gene flow among isolated populations is expected with greater distance and time since fragmentation. Changes in the structure, density, or community composition in the remaining habitats often result in species‘ modifications of vocalizations and morphological traits. However, the relationship between genetic, vocalizations and morphological divergence in urban areas over time remains poorly understood. We analyzed ten years of genetic, acoustic, and morphological data from isolated populations of the white-eared ground-sparrow. We used seven microsatellites (SSRs), recorded, and measured five acoustic traits, and measured six morphological traits, and compared them over a period of ten years. We found an increase in inbreeding, increase in song duration, number of elements, and frequency of maximum amplitude, but a reduction in female body size and changes in male beak. However, we only identified a significant correlation between genetic diversity and the acoustic characteristics of song.

After establishing secondary contact, recently diverged populations may remain reproductively isolated or hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the Variable Seedeater (Sporophila corvina), to examine how coloration and genetic divergence shape patterns of hybridization. We found that plumage coloration has limited introgression across contact zones, but the degree of plumage divergence does not explain overall patterns of introgression. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage) populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting that hybrids present similar or higher fitness than parental subspecies. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic diversity between populations. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.