Data and code from: Spatially heterogeneous gene flow may hinder linking phylogeographic data to macroevolutionary patterns

Biogeography relies on estimates of phylogeny and gene flow to test hypotheses. Established theory posits (1) gene flow varies non-randomly with respect to geography and (2) gene flow can mislead phylogenetic inference. These findings, often viewed in isolation, together suggest that spatial impacts on gene flow could bias biogeographic inference. For example, whenever a “peripheral” population is isolated and inferred as sister to a “core” clade of adjacent populations that exchange migrants, it might reflect elevated gene flow of “core” populations rather than macroevolutionary processes (e.g., direction of colonization). Given this ubiquitous but often unacknowledged biogeographic setting, it remains unknown how spatial influences on gene flow impact metrics used to assess biogeographic hypotheses (e.g., branch length or monophyly). We simulate gene flow that varies nonrandomly regarding geography and found that relatively low levels of gene flow lead to monophyly of adjacent populations, with longer branches for peripheral populations, regardless of true divergence history. We highlight an empirical example wherein antbirds (Thamnophilidae) are young in Amazonia, but older at Amazonia’s periphery. Although it is unclear if the simulated bias applies to antbirds, our results suggest a distinguishability problem for any nodes stemming from radiations in geographically heterogeneous environments.