Time in allopatry does not predict the outcome of secondary contact in lowland Panamanian birds

Geographic speciation models assume that time in allopatry should result in greater reproductive isolation between populations. Here we test the prediction that greater time in allopatry results in greater reproductive isolation using comparative ultraconserved element (UCE) data from ten bird lineages in secondary contact in Panama, measuring both genome-wide divergence and the geographic extent of hybridization. The best-fit models for the proportion of fixed Z-linked and autosomal loci to our data includes a combination of both time (as measured by mtDNA divergence) and hand-wing index, emphasizing that the role of time is tempered by dispersal capability. Furthermore, time does not predict the extent of genome-wide introgression as measured by the median width of diagnostic loci clines or the degree of variation in cline centers or widths. These metrics of the outcome of secondary contact were best predicted by ecological and genomic factors, including diet, hand-wing index, and genome-wide FST respectively, that are understood to serve as proxies for dispersal, the variability of population size, and overall genomic divergence. We find a primary role for ecological factors instead of isolation time in determining secondary contact outcomes for a lineage, highlighting how ecology shapes the development of reproductive isolation.